Import a .mhx file and export it to .bvh problem
I think the simple answer to this is just to save your work as a blender file, i.e. .blend.

I could not find a better way of getting around importing a .mhx file, and then .bvh file and saving my work, so I can reload it later?

As was explained here BVH Export/Import, Armature different when re-imported , blender files encode more information than bvh files so it make sense to save in blender format.